gatk-3.8

Author	SHA1	Message	Date
hanna	a4b69d0adf	Misc bug fixes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2501 348d0f76-0448-11de-a6fe-93d51630548a	2010-01-05 14:48:19 +00:00
hanna	29c129aced	Added very primitive read fishing walker with lots of hard coding. Fixed bugs encountered when testing read fishing in Ecoli. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2496 348d0f76-0448-11de-a6fe-93d51630548a	2010-01-04 00:54:57 +00:00
hanna	b6ecc9e151	Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out and the data backing it up deleted without my knowledge. Unfortunately, since the data was deleted, I had to regenerate the data and a new md5. Hopefully the aligner output is still correct. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2493 348d0f76-0448-11de-a6fe-93d51630548a	2010-01-02 20:19:14 +00:00
hanna	4fbb6d05d0	Refactoring. Push the revisions to the common aligner interface down into the aligner base classes. Hack the managed implementation to support the new interface. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2103 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-20 17:08:09 +00:00